scholarly journals A novel conserved family of Macro-like domains—putative new players in ADP-ribosylation signaling

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6863 ◽  
Author(s):  
Małgorzata Dudkiewicz ◽  
Krzysztof Pawłowski
Keyword(s):  
Functional Data ◽  
Inflammatory Diseases ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Post Translational Modification ◽  
Reading Frame ◽  
Adp Ribosylation ◽  
Mapping Sequence ◽  
Sequence Similarity Analysis

The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers a full understanding of the functioning of living cells. One such example is the human protein C12ORF4, which belongs to the DUF2362 family, present in many eukaryotic lineages and conserved in metazoans. The only functional information available on C12ORF4 (Chromosome 12 Open Reading Frame 4) is its involvement in mast cell degranulation and its being a genetic cause of autosomal intellectual disability. Bioinformatics analysis of the DUF2362 family provides strong evidence that it is a novel member of the Macro clan/superfamily. Sequence similarity analysis versus other representatives of the Macro superfamily of ADP-ribose-binding proteins and mapping sequence conservation on predicted three-dimensional structure provides hypotheses regarding the molecular function for members of the DUF2362 family. For example, the available functional data suggest a possible role for C12ORF4 in ADP-ribosylation signaling in asthma and related inflammatory diseases. This novel family appears to be a likely novel ADP-ribosylation “reader” and “eraser,” a previously unnoticed putative new player in cell signaling by this emerging post-translational modification.

scholarly journals BLASTing away preconceptions in crystallization trials

2019 ◽  
Vol 75 (3) ◽  
pp. 184-192 ◽  
Author(s):  
Gabriel Jan Abrahams ◽  
Janet Newman
Keyword(s):  
Protein Data Bank ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Protein Sequences ◽  
Protein Molecule ◽  
Data Bank ◽  
Dimensional Structure ◽  
Critical Step ◽  
Quantitative Verification ◽  
Better Than

Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption. This research investigates whether, given current information, one can detect any correlation between sequence similarity and crystallization cocktails. BLAST was used to quantitate the similarity between protein sequences in the Protein Data Bank, and this was compared with three estimations of the chemical similarities of the respective crystallization cocktails. No correlation was detected between proteins of similar (but not identical) sequence and their crystallization cocktails, suggesting that methods of determining screens based on this assumption are unlikely to result in screens that are better than those currently in use.

scholarly journals Identification of a positive regulator of the cell cycle ubiquitin-conjugating enzyme Cdc34 (Ubc3).

1996 ◽  
Vol 16 (2) ◽  
pp. 677-684 ◽  
Author(s):  
J A Prendergast ◽  
C Ptak ◽  
D Kornitzer ◽  
C N Steussy ◽  
R Hodgins ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Amino Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Temperature Sensitive ◽  
Reading Frame ◽  
Positive Regulator ◽  
Morphological Defects ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

The Cdc34 (Ubc3) ubiquitin-conjugating enzyme from Saccharomyces cerevisiae plays an essential role in the progression of cells from the G1 to S phase of the cell division cycle. Using a high-copy suppression strategy, we have identified a yeast gene (UBS1) whose elevated expression suppresses the conditional cell cycle defects associated with cdc34 mutations. The UBS1 gene encodes a 32.2-kDa protein of previously unknown function and is identical in sequence to a genomic open reading frame on chromosome II (GenBank accession number Z36034). Several lines of evidence described here indicate that Ubs1 functions as a general positive regulator of Cdc34 activity. First, overexpression of UBS1 suppresses not only the cell proliferation and morphological defects associated with cdc34 mutants but also the inability of cdc34 mutant cells to degrade the general amino acid biosynthesis transcriptional regulator, Gcn4. Second, deletion of the UBS1 gene profoundly accentuates the cell cycle defect when placed in combination with a cdc34 temperature-sensitive allele. Finally, a comparison of the Ubs1 and Cdc34 polypeptide sequences reveals two noncontiguous regions of similarity, which, when projected onto the three-dimensional structure of a ubiquitin-conjugating enzyme, define a single region situated on its surface. While cdc34 mutations corresponding to substitutions outside this region are suppressed by UBS1 overexpression, Ubs1 fails to suppress amino acid substitutions made within this region. Taken together with other findings, the allele specificity exhibited by UBS1 expression suggests that Ubs1 regulates Cdc34 by interaction or modification.

scholarly journals Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation

2009 ◽  
Vol 83 (20) ◽  
pp. 10719-10736 ◽  
Author(s):  
Corinne Rancurel ◽  
Mahvash Khosravi ◽  
A. Keith Dunker ◽  
Pedro R. Romero ◽  
David Karlin
Keyword(s):  
De Novo ◽  
Three Dimensional ◽  
Structural Disorder ◽  
Dimensional Structure ◽  
Overlapping Genes ◽  
Reading Frame ◽  
Sequence Composition ◽  
Overlapping Reading Frames ◽  
Almost All ◽  
Novel Protein

ABSTRACT It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called “overprinting.” To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.

Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart

2014 ◽  
Vol 70 (2) ◽  
pp. 242-252 ◽  
Author(s):  
Sonia Fieulaine ◽  
Michel Desmadril ◽  
Thierry Meinnel ◽  
Carmela Giglione
Keyword(s):  
Sequence Similarity ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Human Counterpart ◽  
Low Activity

Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of theN-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeablein vivoand display similar propertiesin vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.

Cloning and Characterization of an Agglutinin Gene from Arisaema lobatum

2005 ◽  
Vol 25 (5-6) ◽  
pp. 345-362 ◽  
Author(s):  
Juan Lin ◽  
Xuanwei Zhou ◽  
Yongzhen Pang ◽  
Han Gao ◽  
Jiong Fei ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Regulation Mechanism ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
Mannose Binding ◽  
Pcr Technology ◽  
Plant Families ◽  
Race Pcr

A novel agglutinin gene was cloned from Arisaema lobatum using SMART RACE-PCR technology. The full-length cDNA of Arisaema lobatum agglutinin (ala) was 1078 bp and contained a 774 bp open reading frame encoding a lectin precursor (proproprotein) of 258 amino acid residues with a 23 aa signal peptide. ALA contained three mannose-binding sites (QXDXNXVXY) with two-conserved domains of 45% identity, ALA-DOM1 and ALA-DOM2. The three-dimensional structure of ALA was very similar to that of GNA (Galanthus nivalis agglutinin). ALA shared varying identities, ranging from 40% to 85%, with mannose-binding lectins from other species of plant families, such as Araceae, Alliaceae, Iridaceae, Lillaceae, Amaryllidaceae and Bromeliaceae. Genomic sequence of ala was also cloned using genomic walker technology, and it was found to contain three putative TATA boxes and eight possible CAAT boxes in the 5′-flanking region. No intron was found within the region of genomic sequence. Southern blot analysis indicated that the ala belonged to a multi-copy gene family. Expression pattern analysis revealed that the ala preferentially expressed in the tissues with the higher expression being found in spadix, bud, leaf, spathe and tuber. The cloning of the ala gene not only provides a basis for further investigation of its structure, expression and regulation mechanism, but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into plants in the future.

scholarly journals Pkg2, a Novel Transmembrane Protein Ser/Thr Kinase of Streptomyces granaticolor

1999 ◽  
Vol 181 (1) ◽  
pp. 15-23 ◽  
Author(s):  
Richard Nádvorník ◽  
Tomáš Vomastek ◽  
Jiří Janeček ◽  
Zuzana Techniková ◽  
Pavel Branny
Keyword(s):  
Amino Acids ◽  
Tandem Repeats ◽  
Transmembrane Protein ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Chromosomal Dna ◽  
Serine Threonine Kinase ◽  
Significant Sequence Similarity ◽  
Threonine Kinase

ABSTRACT A 4.2-kb SphI-BamHI fragment of chromosomal DNA from Streptomyces granaticolor was cloned and shown to encode a protein with significant sequence similarity to the eukaryotic protein serine/threonine kinases. It consists of 701 amino acids and in the N-terminal part contains all conserved catalytic domains of protein kinases. The C-terminal domain of Pkg2 contains seven tandem repeats of 11 or 12 amino acids with similarity to the tryptophan-docking motif known to stabilize a symmetrical three-dimensional structure called a propeller structure. The pkg2 gene was overexpressed inEscherichia coli, and the gene product (Pkg2) has been found to be autophosphorylated at serine and threonine residues. The N- and C-terminal parts of Pkg2 are separated with a hydrophobic stretch of 21 amino acids which translocated a PhoA fusion protein into the periplasm. Thus, Pkg2 is the first transmembrane protein serine/threonine kinase described for streptomycetes. Replacement of the pkg2 gene by the spectinomycin resistance gene resulted in changes in the morphology of aerial hyphae.

scholarly journals Solution Structure of Acidocin B, a Circular Bacteriocin Produced by Lactobacillus acidophilus M46

2015 ◽  
Vol 81 (8) ◽  
pp. 2910-2918 ◽  
Author(s):  
Jeella Z. Acedo ◽  
Marco J. van Belkum ◽  
Christopher T. Lohans ◽  
Ryan T. McKay ◽  
Mark Miskolzie ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lactobacillus Acidophilus ◽  
Solution Structure ◽  
Sequence Similarity ◽  
Sodium Dodecyl ◽  
Three Dimensional ◽  
Peptide Sequence ◽  
Dimensional Structure ◽  
Content Type ◽  
Circular Bacteriocin

ABSTRACTAcidocin B, a bacteriocin produced byLactobacillus acidophilusM46, was originally reported to be a linear peptide composed of 59 amino acid residues. However, its high sequence similarity to gassericin A, a circular bacteriocin fromLactobacillus gasseriLA39, suggested that acidocin B might be circular as well. Acidocin B was purified from culture supernatant by a series of hydrophobic interaction chromatographic steps. Its circular nature was ascertained by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry and tandem mass spectrometry (MS/MS) sequencing. The peptide sequence was found to consist of 58 amino acids with a molecular mass of 5,621.5 Da. The sequence of the acidocin B biosynthetic gene cluster was also determined and showed high nucleotide sequence similarity to that of gassericin A. The nuclear magnetic resonance (NMR) solution structure of acidocin B in sodium dodecyl sulfate micelles was elucidated, revealing that it is composed of four α-helices of similar length that are folded to form a compact, globular bundle with a central pore. This is a three-dimensional structure for a member of subgroup II circular bacteriocins, which are classified based on their isoelectric points of ∼7 or lower. Comparison of acidocin B with carnocyclin A, a subgroup I circular bacteriocin with four α-helices and a pI of 10, revealed differences in the overall folding. The observed variations could be attributed to inherent diversity in their physical properties, which also required the use of different solvent systems for three-dimensional structural elucidation.

scholarly journals The Rib43a Protein Is Associated with Forming the Specialized Protofilament Ribbons of Flagellar Microtubules inChlamydomonas

2000 ◽  
Vol 11 (1) ◽  
pp. 201-215 ◽  
Author(s):  
Jan M. Norrander ◽  
Aimee M. deCathelineau ◽  
Jennifer A. Brown ◽  
Mary E. Porter ◽  
Richard W. Linck
Keyword(s):  
Homo Sapiens ◽  
Sequence Similarity ◽  
Germ Cell Tumors ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Dimensional Structure ◽  
Polymorphism Analysis ◽  
Basal Bodies ◽  
Coding Region ◽  
Expression Library

Ciliary and flagellar microtubules contain a specialized set of three protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. Previous studies of sea urchin sperm flagella identified three of the ribbon proteins astektins, which form coiled-coil filaments in doublet microtubules and which are associated with basal bodies and centrioles. To study the function of tektins and other ribbon proteins in the assembly of flagella and basal bodies, we have begun an analysis of ribbons from the unicellular biflagellate, Chlamydomonas reinhardtii, and report here the molecular characterization of the ribbon protein rib43a. Using antibodies against rib43a to screen an expression library, we recovered a full-length cDNA clone that encodes a 42,657-Da polypeptide. On Northern blots, the rib43a cDNA hybridized to a 1.7-kb transcript, which was up-regulated upon deflagellation, consistent with a role for rib43a in flagellar assembly. The cDNA was used to isolate RIB43a, an ∼4.6-kb genomic clone containing the complete rib43a coding region, and restriction fragment length polymorphism analysis placed the RIB43agene on linkage group III. Sequence analysis of theRIB43a gene indicates that the substantially coiled-coil rib43a protein shares a high degree of sequence identity with clones from Trypanosoma cruzi and Homo sapiens(genomic, normal fetal kidney, and endometrial and germ cell tumors) but little sequence similarity to other proteins including tektins. Affinity-purified antibodies against native and bacterially expressed rib43a stained both flagella and basal bodies by immunofluorescence microscopy and stained isolated flagellar ribbons by immuno-electron microscopy. The structure of rib43a and its association with the specialized protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilizing doublet and triplet microtubules and in organizing their three-dimensional structure.

scholarly journals Signals Getting Crossed in the Entanglement of Redox and Phosphorylation Pathways: Phosphorylation of Peroxiredoxin Proteins Sparks Cell Signaling

Antioxidants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 29 ◽  
Author(s):  
John Skoko ◽  
Shireen Attaran ◽  
Carola Neumann
Keyword(s):  
Cell Signaling ◽  
Cell Fate ◽  
Intracellular Signaling ◽  
Redox Homeostasis ◽  
Three Dimensional ◽  
Cysteine Residue ◽  
Signaling Cascades ◽  
Dimensional Structure ◽  
Post Translational Modification ◽  
Downstream Signaling

Reactive oxygen and nitrogen species have cell signaling properties and are involved in a multitude of processes beyond redox homeostasis. The peroxiredoxin (Prdx) proteins are highly sensitive intracellular peroxidases that can coordinate cell signaling via direct reactive species scavenging or by acting as a redox sensor that enables control of binding partner activity. Oxidation of the peroxidatic cysteine residue of Prdx proteins are the classical post-translational modification that has been recognized to modulate downstream signaling cascades, but increasing evidence supports that dynamic changes to phosphorylation of Prdx proteins is also an important determinant in redox signaling. Phosphorylation of Prdx proteins affects three-dimensional structure and function to coordinate cell proliferation, wound healing, cell fate and lipid signaling. The advent of large proteomic datasets has shown that there are many opportunities to understand further how phosphorylation of Prdx proteins fit into intracellular signaling cascades in normal or malignant cells and that more research is necessary. This review summarizes the Prdx family of proteins and details how post-translational modification by kinases and phosphatases controls intracellular signaling.

scholarly journals Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Karine de Guillen ◽  
Cécile Lorrain ◽  
Pascale Tsan ◽  
Philippe Barthe ◽  
Benjamin Petre ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Sequence Similarity ◽  
Rust Fungus ◽  
Parasitic Infection ◽  
Three Dimensional ◽  
Effector Proteins ◽  
Host Cells ◽  
Dimensional Structure ◽  
Small Proteins ◽  
Wide Range

AbstractRust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we produced recombinant proteins of eleven candidate effectors of the leaf rust fungus Melampsora larici-populina in Escherichia coli. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both MLP124266 and MLP124017 show no sequence similarity with known proteins, they exhibit structural similarities to knottins, which are disulfide-rich small proteins characterized by intricate disulfide bridges, and to nuclear transport factor 2-like proteins, which are molecular containers involved in a wide range of functions, respectively. Interestingly, such structural folds have not been reported so far in pathogen effectors, indicating that MLP124266 and MLP124017 may bear novel functions related to pathogenicity. Our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize effector candidates.

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